Aging is a process in which all individuals of a species undergo a progressive decline in vitality leading to death. In metazoans, aging at the level of the whole organism is clearly evident. Whether the aging of an organism is genetically programmed, or represents the effects of entropy over time is not clear. Consistent with the possibility of a genetic program are mutations which alter the aging process. In humans the genetic diseases progeria and Werner""s syndrome cause premature aging in affected individuals. In the earthworm C. elegans, a gene, age-1, has been described which directly or indirectly affects the life span of the animal (Friedman, D. B. and Johnson, T. E., Genetics 18:75-86 (1988)). A further issue open to speculation is how the aging of the entire organism relates to the aging of individual cells and cell types within the organism.
That individual cells within mammals do senesce was demonstrated in the findings of Hayflick, who showed that primary human diploid fibroblasts (HDFs) would grow in culture for about 50 population doublings, and then all the cells in the population would stop dividing (Hayflick, L. and Moorhead, P. S., Exp. Cell Res. 25:585-621 (1961); Hayflick, L., Exp. Cell Res. 37:614-636 (1965)). Cells arrest in the G1 phase of the cell cycle and contain a 2N chromosomal complement (Cristofalo, V. J., et al., Exp. Gerontol. 24:367 (1989)). This in phase, or clonal, senescence of the HDFs is accompanied by a characteristic morphological change; cells enlarge as they senesce (Angello, J. C., et al., J. Cell. Physiol. 132:125-130 (1987) and Cristofalo, V. J. and Kritchevsky, D., Med. Exp. 19:313-320 (1969)). In fact, this direct correlation between cell size and senescence can be demonstrated by incubating young HDFs in low serum-medium, in which they enlarge, but do not leave the G1 phase of the cell cycle (Angello, J. C., et al., J. Cell. Physiol. 140:288-294 (1989)). When these cells are returned to medium containing adequate serum for cell division, their program of senescence has been advanced compared to smaller cells which have divided the same number of times.
Cell fusion studies between old and young HDFs indicate that senescence is dominant. In short term hybrids, initiation of DNA synthesis in the young nucleus is inhibited after the young cell has been fused to a senescent HDF (Norwood, T. H., et al., Proc. Natl. Acad. Sci. USA 71:2231 (1974)). In fact, injection of polyA+ RNA from the senescent HDF into the young cell inhibits DNA synthesis (Lumpkin, C. K., Jr., et al., Science 232:393 (1986)), suggesting that the senescent HDF activated a gene or genes that encoded dominant inhibitory proteins. In complementation studies that involve fusing various xe2x80x9cimmortalxe2x80x9d cell lines, four genes were identified which were involved in immortalization (Pereira-Smith, O. M. and Smith, J. R., Proc. Natl. Acad. Sci. USA 785:6042 (1988)). The dominance of senescence appears to conflict with the view that shortening of telomeres, a phenomenon observed during passage of fibroblasts (Harley, C. B., et al., Nature 345:458 (1990)), causes senescence.
In several lower eukaryotes, senescence has been demonstrated and linked to changes in mitochondria. In Podospora, cell senescence is strongly associated with the excision and amplification of segments of mitochondrial DNA (Cummings, D. J., et al., J. Mol. Biol. 185:659-680 (1985) and Koll, F. et al., Plasmid 14:106-117 (1985)). In Neurospora (Bertrand J., et al., Cell 47:829-837 (1986)) and Aspergillus (Lazarus, C. M., et al., Eur. J. Biochem 106:663-641 (1989)), senescent cells also contain rearrangements in their mitochondrial DNA. In all of the above examples, the senescent phenotype is dominant and is inherited cytoplasmically.
In the budding yeast, Saccharomyces cerevisiae, cells divide asymmetrically, giving rise to a large mother cell and a small daughter cell. By micromanipulating the daughter away from the mother at each cell division, it was shown that the mother divided a fixed number of times, and then stopped (Mortimer, R. K. and Johnston, J. R., Nature 183:1751-1752 (1959)). Life span was thus defined by the number of divisions mother cells had undergone, and not by chronological time. Further, a number of cell divisions in the life span of the mother, while fixed (varying over a Gompertz distribution (Pohley, J.-J. Mech. Ageing Dev. 38:231-243 (1987)), could differ from strain to strain (ranging from about 15 to 30) (Egilmez, N. K. and Jazwinski, S. M., J. Bacteriol. 171:37-42 (1989)). Thus, senescence in budding yeast as in HDFs is not a stochastic process, but has some underlying genetic basis.
Senescence in yeast is like senescence in HDFs in other ways as well. Like HDFs, yeast mother cells have been shown to enlarge with age (Mortimer, R. K. and Johnston, J. R., Nature 183:1751-1752 (1959) and Egilmez, N. K., et al., J. Gerontol. Biol. Sci. 45:B9-17 (1990)). In addition to their large size, aging mother cells also divide more slowly than young cells (Egilmez, N. K. and Jazwinski, S. M., J. Bacteriol. 171:37-42 (1989)). A further analogy to HDFs is that the senescent phenotype is also dominant in yeast. Mating a young yeast cell to an old one generates a diploid with a limited potential for cell division (Muller, I., J. Microbiol. Serol. 51:1-10 (1985)). In addition, daughters of old mothers display elongated cycling times for the first few divisions after separation from the old mother (Egilmez, N. K. and Jazwinski, S. M., J. Bacteriol. 171:37-42 (1989)). Evidently, the senescence substance is inherited by the daughter cell and slowly degraded or diluted in subsequent cell cycles.
The senescence of yeast mother cells thus has similarities to what occurs in primary HDFs; however, there is one important difference. In yeast at each cell division the daughter cell has regained the capacity for a full life span, whether derived from a younger or older mother cell (Muller, I., Arch. Mikrobiol. 77:20-25 (1971)). This xe2x80x9cresettingxe2x80x9d in daughters may be intertwined with the mechanism that generates asymmetry at cell division. In any case, xe2x80x9cresettingxe2x80x9d argues against one category of hypothesis for aging; namely that aging results from the accumulation of errors in protein synthesis, the error catastrophe theory (Orgel, L. E. Nature 243:441 (1973)). Because daughter cells derived from old mothers have functional mitochondria (Muller, I. and Wolf, F., Mol. Gen. Genet. 160:231-234 (1978)), this resetting also shows that senescence is not due to rearrangements in the mitochondrial genome.
By varying the growth rate of cells, it was demonstrated that the key parameter in determining the life span in yeast is number of divisions, and not chronological time (Muller, I., et al., Mech. Ageing Dev. 12:47-52 (1980)). This finding led to the idea that senescence could be due to an accumulation of bud scars in mother cells. Bud scars are deposits of chitin that stay with the mother cell after each cell division (Cabib, E., et al., Curr. Top. Cell. Regul. 8:1-32 (1974), and Pringle, J. R., et al., Meth. Cell Biol. 31:357-435 (1989)). Several lines of evidence have argued against the idea that bud scars cause aging. First, varying the surface to volume ratio of isogenic yeast strains by varying their ploidy did not affect life span (Muller, I., Arch. Mikrobiol. 77:20-25 (1971)). Second, increasing the surface area by mating an old cell to a young one did not endow the diploid with an increased potential for division (Muller, I., J. Microbiol. Serol. 51:1-10 (1985)). Third, induction of chitin synthesis and deposition in the cell wall did not decrease the life span of cells (Egilmez, N. K. and Jazwinski, S. M., J. Bacteriol. 171:37-42 (1989)). Thus, senescence in yeast has gross features similar to the aging process in mammalian cells. It is therefore reasonable to speculate that the molecular mechanisms of aging might be similar in yeast and mammalian cells, particularly in light of striking parallels in basic cellular mechanisms in yeast and mammalian cells. In the field of transcription, for example, there has emerged strong mechanistic similarities in the function of transcription factors: the yeast and mammalian TATA box binding factor TFID, are interchangeable in the basal in vitro transcription reaction (Buratowski, S., et al., Nature 334:37-42 (1988)). Further, yeast and certain mammalian transcriptional activators will function normally in the heterologous host cells (see Guarente, L., et al., Cell 52:303-305 (1988) for review). Therefore, further study of aging in yeast cells may yield information concerning genes which are involved in senescence, and ultimately may shed light on the aging process in mammalian cells.
The present invention pertains to life span-determining genes which affect senescence in eukaryotic cells, such as budding yeast, and to mutated forms of the life span-determining genes. The genes of the present invention affect senescence either by contributing to aging or by conferring an extended life span upon the eukaryotic cell. Mutated genes of the present invention differ from wild type or naturally-occuring genes in that there is an addition, deletion, substitution or other alteration of the nucleic acid sequence, with the result that the encoded protein differs from the protein encoded by the non-mutated (wild-type) gene in at least one amino acid.
As described herein, it was discovered that the SIR4 gene (silent information regulator) contributes to extended life span: when the SIR4 gene is deleted, the resulting mutant yeast cells have a significantly shorter life span than yeast cells which contain the SIR4 gene. However, when mutant yeast cells are generated by a specific mutation in the SIR4 gene, the resultant mutant cells have a life span that is significantly longer than the life span of the non-mutant strain. The mutation is an amber mutation that removes 121 residues from the 1358 residue SIR4 protein.
It has also been discovered that the UTH4 gene affects senescence in a manner similar to that of SIR4. That is, a particular mutation in the UTH4 gene confers extended life span on mutant yeast cells.
As further described herein, it was discovered that the UTH1 gene effects senescence by contributing to the aging process. In particular, deletion of the UTH1 gene confers extended life span on the mutant yeast cell compared with the life span exhibited by yeast cells which contain the UTH1 gene.
Additional genes have been identified which show strong homology to the UTH4 and UTH1 genes. In particular, the yeast YGL023 and Drosophila PUMMILIO gene, as well as the human D43951 and D13645 genes, show strong homology to UTH4. The yeast NCA3 gene and the SAG1 gene show strong homology to the UTH1 gene. Deletion of either the NCA3 or SAG1 gene result in shortened yeast cell life span compared with wild-type (non-deleted) yeast cells. This indicates that NCA3 and SAG1 are genes which contribute to extended life span in yeast.
As a result of these discoveries, methods of isolating mutant yeast cells with increased life span, and the mutant yeast cells isolated by these methods, are now available. Also available are methods to identify agents which enhance the life span of yeast cells; methods to isolate genes involved in senescence, as well as the genes isolated thereby, and the proteins encoded by the genes.
As described in detail below, the current invention comprises several methods of isolating yeast cells with increased life spans (a life span longer than the known life span of the non-mutagenized yeast strain). In each method, a sample of yeast cells from a budding yeast strain, for which the life span is known or has been calculated, is exposed to a mutagen, and then the mutagen-exposed yeast cells are cultured. In one embodiment of the current invention, mutant yeast cells are identified first by the related phenotype of starvation resistance. The yeast cells are plated on minimal medium, replica-plated on starvation medium, and grown. The plate with starvation medium is replica-plated to enriched medium; those colonies which grow are starvation resistant. The starvation-resistant colonies are then examined to isolate cells with longer life spans.
In a second embodiment, the cell surface of yeast cells are labelled with a fluorescent marker. New cells remain unlabelled. After a period of growth greater than the known life span of the yeast strain, the cells are subjected to fluorescence-activated cell sorting to isolate the fluorescent-labelled cells, which are then plated. Only those cells with longer life spans grow. In another embodiment, a temperature-sensitive budding yeast strain, in which the daughter cells die at the non-permissive temperature, is used. When cells from the temperature-sensitive strain are grown at the non-permissive temperature, they form microcolonies in which the number of cells in the microcolony is equivalent to the number of generations in the life span of the yeast strain. Larger microcolonies, which are comprised of cells with a longer life span, are identified. Cells with increased life spans, isolated by any of these methods, are also part of the current invention.
The current invention also comprises methods of identifying agents which increase life span. Cells from a budding yeast strain with a known life span are exposed to the agent to be tested; the cells are then cultured and examined to determine whether they have longer life spans, using any of the methods described above. The presence of cells having longer life spans is indicative of the ability of the agent to increase life span of the cells.
In addition, the current invention pertains to genes which are involved in senescence of organisms, including yeast, bacteria and vertebrates, particularly mammals. Genes can be isolated by complementation analysis. For example, a genomic DNA library is constructed for the organism of interest, and is transformed into a mutant yeast strain having a mutated gene which contributes to longer life span, such as a mutant SIR4 gene. The DNA from the organism of interest is then isolated from those transformants which have the usual life span (i.e., those cells from the mutant yeast strain which no longer have a longer life span).
Alternatively, genes which are homologous to and/or hybridize to a gene that is known to affect senescence, such as SIR4, can be identified and/or isolated. The isolated genes, and the proteins encoded by the genes, are also the subject of the current invention. The subject invention also relates to DNA which encodes a protein which affects senescence in an organism (eukaryotes such as yeast and mammals, including humans, and prokaryotes). This includes UTH1 (SEQ ID NO. 1), DNA which is homologous to and/or hybridizes to UTH1, such as NCA3 (SEQ ID NO. 11) and SAG1 (SEQ ID NO. 13), and DNA which encodes the same amino acid sequence as that encoded by UTH1, NCA3 or SAG1. This invention also relates to UTH1, NCA3 or SAG1 DNA which has been mutated, including mutations which cause non-expression of the encoded protein, DNA which is homologous to and/or hybridizes to the mutant UTH1, NCA3 or SAG1 DNA, and DNA which encodes the same amino acid sequence as that encoded by mutant UTH1, NCA3 or SAG1 DNA. This invention also includes proteins encoded by UTH1, NCA3 or SAG1 DNA and similar DNA sequences, as well as to proteins encoded by mutated UTH1, NCA3 or SAG1 DNA.
This invention also pertains to the UTH4 gene (SEQ ID NO. 3), DNA which is homologous to and/or hybridizes to UTH4, such as YGL023 (SEQ ID NO. 5), D43951 (SEQ ID NO. 7, FIGS. 18A-G) and D13645 (SEQ ID NO. 9), and DNA which encodes the same amino acid sequence as that encoded by UTH4, YGL023, D43951 or D13645. Also included is UTH4, YGL023, D43951 and D13645 DNA which has been mutated, including mutations which cause non-expression of the encoded protein or mutations which encode a stop codon, DNA which is homologous to and/or hybridizes to the mutant UTH4, YGL023, D43951 or D13645 DNA, and DNA which encodes the same amino acid sequence as that encoded by mutant UTH4, YGL023, D43951 or D13645 DNA. Further included are proteins encoded by UTH4, YGL023, D43951 and D13645 DNA and similar DNA sequences, as well as to proteins encoded by mutated UTH4, YGL023, D43951 or D13645 DNA.
Further, this invention includes DNA which is homologous to and/or hybridizes to SIR4 and DNA which encodes the same amino acid sequence as that encoded by SIR4. It also relates to mutant SIR4 DNA (which includes a stop codon at amino acid 1237 of the encoded protein), DNA which is homologous to and/or hybridizes to the mutant SIR4 DNA, and DNA which encodes the same amino acid sequence as that encoded by mutant SIR4 DNA. The present invention also relates to proteins encoded by mutant SIR4 DNA and the similar mutant SIR4 DNA sequences.